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If no leaving group is found, after you enter ’)’, a dialog box will prompt you to specify the attachment point.
You can expand and contract protected residues just as any other residues.
Pasting sequences
You can now paste sequences in FASTA format. Since only single-letter IUPAC codes are present in the FASTA for-
mat, you must indicate whether this corresponds to a peptide, DNA, or RNA biopolymer sequence. You can paste
ALL IUPAC symbols for residues, with the exception of those characters indicating spaces or omissions.
To paste a sequence:
Right-click and go to the Paste Special sub menu.
ChemBioDraw 13.0
Chapter 5: Drawing biopolymers 63 of 401
- ChemBioDraw 13.0 User Guide 1
- Table of Contents 2
- Table of Contents ii 3
- Table of Contents iii 4
- Table of Contents iv 5
- Table of Contents v 6
- What’s new 7
- What’s new vii 8
- What’s new viii 9
- Introduction 10
- Troubleshooting 11
- Performance 11
- Applications and drivers 12
- Getting started 13
- Toolbars 14
- Documents 15
- Deleting a keyword 16
- Discarding changes 16
- Undo, redo, and repeat 16
- Saving documents 16
- Autosave 17
- Default file format 17
- Dropbox interface 17
- Signing into Dropbox 17
- Upload files 18
- Download files 19
- Basic drawings 21
- Quadruple bonds 22
- Dative bonds 22
- Wedged bonds 22
- Changing bonds 22
- Changing bond types 23
- Changing double bonds 23
- Aligning double bonds 23
- Moving atoms 23
- Reducing ring size 24
- Bond crossing 24
- Fixed bonds 24
- Drawing fixed length bond 24
- Drawing fixed angle bonds 24
- Changing fixed values 25
- Periodic table 25
- Captions 26
- Formatting 27
- Coloring text 28
- Caption width 29
- About fonts 29
- Character map 29
- Using hotkeys 30
- Nicknames 31
- Using nicknames 31
- Applying nicknames 31
- Expanding nicknames 32
- Annotations 33
- Drawing rings 35
- Spiro and sprout rings 36
- Cyclohexane chair rings 36
- Aromatic structures 37
- Delocalized rings 37
- Resonance structures 37
- Changing chain direction 38
- Fixed length 38
- Fixed angle 38
- Adding chains to structures 38
- Specifying chain length 38
- Arrow heads 39
- Arrow types 39
- Hollow arrows 40
- Connecting arrows 41
- Curved arrows 42
- Colored arrows 42
- Coloring block arrows 42
- Drawing elements 43
- Circles and ovals 43
- Brackets 44
- Freehand shapes 46
- Selecting objects 47
- The lasso tool 47
- The marquee tool 47
- Selecting entire structures 48
- Selecting objects by clicking 48
- Selecting multiple objects 48
- Deselecting all objects 48
- Deselecting one object 48
- Resizing objects 49
- Rotating objects 50
- Moving the center of rotation 50
- Moving objects 51
- Copying objects 51
- The info window 52
- Mirror images 52
- Deleting objects 53
- Joining structures 53
- Grouping objects 53
- Ungrouping objects 54
- Scaling objects 54
- Centering objects 55
- Aligning objects 55
- Distributing objects 55
- Clean Up Structure 56
- Check structure 57
- Chemical warnings 57
- Warning preferences 58
- Warning Description 59
- Linear Atom 59
- BioDraw templates 60
- Advanced BioDraw 61
- Anatomy templates 61
- Bio Instruments 62
- Microorganisms 62
- Organelles 62
- Customizable objects 63
- Membrane line 64
- Membrane arc 64
- Helix proteins 64
- DNA molecules 65
- Coloring residues 65
- Ribosomes 66
- Plasmid maps 66
- Creating a plasmid map 66
- Adding regions 67
- Adding markers 67
- Moving markers 67
- Resizing regions 67
- Enhancing the drawing 68
- Drawing biopolymers 69
- Biopolymer editor 70
- Protecting groups 71
- Pasting sequences 72
- Paste text strings 73
- Expanding sequences 74
- Contracting labels 74
- Modifying sequence residues 74
- Removing residues 76
- Replacing residues 77
- Adding residues 77
- Hybrid biopolymers 78
- IUPAC codes 79
- Branched peptides 82
- Disulfide bridges 83
- Lactam bridges 84
- Tutorials 86
- Tutorial 2: Drawing rings 87
- The structure is complete 89
- Drawing the Newman projection 98
- Tutorial 6: Stereochemistry 99
- Adding atom labels 100
- Tutorial 7: Templates 102
- Advanced drawing techniques 104
- Creating labels 105
- Expanding labels 106
- Multiple atoms 106
- Attachment points 108
- Atom numbering 110
- Structure perspective 111
- Mass fragmentation 112
- Drawing reactions 113
- Drawing an arrow 114
- Drawing the product 114
- Clean Up Reaction 116
- The reaction interpreter 117
- Electron and radical pushing 118
- Stoichiometry grid 119
- Templates 122
- Customizing templates 123
- Modifying a template 123
- Adding a template 123
- Annotating a template 123
- Defining nicknames 124
- Nicknames and atom labels 126
- Deleting nicknames 126
- Troubleshooting nicknames 126
- ChemScript 127
- Struct=Name 129
- Non-ringed structures 130
- Ringed structures 130
- Fused ring systems 131
- Bridged fused ring systems 131
- Polymers 132
- Other compounds 132
- Unsupported structures 132
- Name>Struct 133
- Converting clipboard names 134
- Converting captions 134
- Supported structures 134
- ChemBioDraw 13.0 135
- Chemistry features 136
- ChemBioFinder hotlink 137
- Stereochemistry 138
- Hiding indicators 139
- Formatting indicators 139
- Removing indicators 139
- Positioning indicators 139
- Relative stereochemistry 140
- Chemical annotations 141
- S-orbitals 142
- Sigma orbitals 142
- Single lobe orbitals 142
- Hybrid orbitals 142
- Chemical symbols 143
- H–dot and H–dash 143
- Lone pair/diradical 143
- Charge symbols 144
- Chemical properties 145
- Boiling point 146
- Critical pressure 147
- Critical temperature 147
- Critical volume 147
- CLogP/CMR 147
- Gibbs free energy 147
- Heat of formation 148
- Henry’s law constant 148
- Melting point 148
- ChemBioFinder properties 151
- Viewing chemical properties 151
- 3D viewing 152
- In the document window 153
- In ChemBio3D preview 153
- Resizing spots 156
- Custom spots 156
- Gel electrophoresis tool 156
- Parameters in ChemNMR 159
- Spectrometer frequency 159
- NMR shifts 160
- Modifying NMR frequency 160
- Viewing spectral assignments 161
- Removing spectral assignments 161
- Custom shift correction data 161
- NMR data format 161
- Updating the ChemNMR database 162
- Restoring default NMR data 162
- Example supplementary data 162
- ChemNMR limitations 164
- NMR references 165
- ChemDraw/Excel 166
- Importing hit lists 167
- Exporting tables 167
- Synchronizing tables 168
- Adding structures 169
- Searching 170
- Opening a database 171
- Normal searches 171
- Similarity searches 171
- R-Group analysis 172
- Working with structures 172
- Using the clipboard 173
- ChemDraw/Excel functions 174
- Chemical name 175
- Chemical composition 175
- Chemical formula 175
- Molecular weight 176
- Exact mass 176
- Number of atoms 176
- SMILES string 177
- Formal charge 177
- Melting/freezing point 178
- Vapor pressure 179
- Ideal gas thermal capacity 180
- Molar refractivity 181
- Water solubility 181
- Balaban index 183
- Cluster count 183
- Topological index 183
- Number of rotatable bonds 184
- Polar surface area 184
- Shape attribute 184
- Shape coefficient 184
- Sum of degrees 185
- Sum of valence degrees 185
- Topological diameter 185
- Total connectivity 185
- Total valence connectivity 185
- Wiener index 186
- Lipinski rule of five 187
- Ghose modifications 187
- Henry’s Law constant 192
- Total Valence Connectivity 196
- CombiChem 197
- Entering a generic reaction 198
- Creating reactant worksheets 199
- Searching for reactants 199
- Creating an experiment 200
- Experiment worksheets 201
- Configuring plates 202
- Assigning plates 202
- Browsing plates 203
- Viewing related structures 203
- ChemBioFinder/Office 204
- Editing the hitlist 205
- ChemDraw for Excel 205
- Query structures 206
- Generic nickname hotkeys 207
- Defining generic nicknames 207
- Atom properties 209
- Query indicators 210
- Positioning query indicators 211
- Hiding a query indicators 211
- Removing atom properties 211
- Atom property options 211
- Substituents 211
- Implicit hydrogens 213
- Ring bond count 213
- Unsaturation 214
- Reaction change 214
- Reaction stereo 214
- Free sites 215
- Translation 216
- Bond properties 217
- Viewing bond properties 218
- Removing bond properties 218
- Bond property options 219
- Bond types 219
- Topology 219
- Element lists 220
- Setting bracket properties 222
- Bracket usage 222
- Structure-based polymers 222
- Source-based polymers 223
- Multiple groups 224
- Link nodes 225
- Alternative groups 226
- Defining alternative groups 227
- Multiple attachment points 229
- Attachment point numbering 230
- Hiding rank indicators 230
- R-group reaction queries 231
- Anonymous alternative groups 232
- Expand generic structures 233
- R-Logic queries 234
- Atom-to-Atom mapping 235
- Displaying and printing 236
- Automatic mapping 236
- Manual mapping 236
- Stereochemical symbols 238
- 3D properties 239
- Export compatibility 240
- Sharing information 244
- Pasting SMILES 245
- Creating SLN strings 245
- Creating InChI™ strings 245
- Creating InChIKey strings 245
- Transferring objects 246
- Embedding objects 247
- Exporting 247
- Importing 248
- ISIS™ compatibility 249
- Attached data 249
- Modifying attached data 249
- File formats 250
- Transferring across platforms 252
- Preferences and settings 253
- Default document location 254
- Default open file format 254
- Setting the default tool 254
- Highlight box tolerance 254
- The ChemDraw items folder 255
- Default styles 255
- Saving customized styles 255
- Setting preferences 256
- Windows XP 258
- Windows Vista 258
- Customizing toolbars 268
- Document and object settings 268
- Drawing settings 269
- Configuring documents 270
- Configuring objects 271
- Analysis and properties 271
- Formatting captions 272
- Style indicators 273
- Specifying line spacing 273
- Aligning text 273
- Automatic alignment 274
- Changing the default format 275
- Biopolymer settings 276
- Customizing hotkeys 277
- {description}”/> 278
- Working with color 279
- Color by element 280
- The color palette 281
- Customizing colors 281
- Document settings 282
- Adv. Synth Catal 283
- J.Chin. Chem. Soc 283
- J. Mol. Mod. (1 column) 284
- New Document 284
- New Slide 284
- Phytomedicine 285
- Science of Synthesis 286
- Synthesis, Synlett 286
- Verlag Helvetica Chimica Acta 287
- Wiley Document 287
- Page layout 288
- Headers and footers 289
- Printing 290
- Saving page setup settings 291
- 35mm slide boundary guides 291
- Viewing drawings 292
- The crosshairs 293
- Moving the crosshair 293
- Positioning objects 293
- Creating a table 293
- Resizing tables 294
- Customizing borders 294
- Using the text tool 295
- Creating a new row 296
- Inserting a new row 296
- Chemical interpretation 297
- Bond conventions 298
- Atom labels 299
- Chemically significant text 301
- Isotopes and elements 302
- Radicals 303
- H-Dot/H-Dash 303
- Complexes 303
- Multi-center attachments 304
- Cahn-Ingold-Prelog 305
- Stereochemical indicators 305
- Stereochemical flags 305
- Polymer representations 307
- References 307
- Analysis messages 307
- Property calculations 310
- The ChemBio3D MOPAC interface 312
- Other properties 312
- Miscellaneous properties 312
- Shortcuts and hotkeys 313
- Bond hotkeys 314
- Function hotkeys 315
- Shortcuts 316
- Structure 318
- Registering online 321
- User’s guide 321
- Technical support 321
- ACX structures and numbers 322
- ACX structures 322
- ACX numbers 322
- ChemBio3D ActiveX Control 322
- SciStore.com 322
- PerkinElmer Informatics 323
- Using the ChemOffice SDK 323
- Index 315 of 401 324
- Index 316 of 401 325
- Index 317 of 401 326
- Index 318 of 401 327
- Index 319 of 401 328
- Index 320 of 401 329
- Index 321 of 401 330
- Index 322 of 401 331
- Index 323 of 401 332
- Index 324 of 401 333
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- Index 341 of 401 350
- Index 342 of 401 351
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- Index 344 of 401 353
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- Index 352 of 401 361
- Index 353 of 401 362
- Index 354 of 401 363
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- Index 391 of 401 400
- Index 392 of 401 401
- Index 393 of 401 402
- Index 394 of 401 403
- Index 395 of 401 404
- Index 396 of 401 405
- Index 397 of 401 406
- Index 398 of 401 407
- Index 399 of 401 408
- Index 400 of 401 409
- Index 401 of 401 410
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